JAL-2446 add call to SequenceFeatures.delete(); use varargs for type

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 68c8c50..e1c8566 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -22,6 +22,7 @@ package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
 import jalview.api.DBRefEntryI;
+import jalview.datamodel.features.SequenceFeatures;
 import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
@@ -81,6 +82,8 @@ public class Sequence extends ASequence implements SequenceI
   /** array of sequence features - may not be null for a valid sequence object */
   public SequenceFeature[] sequenceFeatures;
 
+  private SequenceFeatures sequenceFeatureStore;
+
   /**
    * Creates a new Sequence object.
    * 
@@ -120,6 +123,7 @@ public class Sequence extends ASequence implements SequenceI
     this.sequence = sequence2;
     this.start = start2;
     this.end = end2;
+    sequenceFeatureStore = new SequenceFeatures();
     parseId();
     checkValidRange();
   }
@@ -233,8 +237,7 @@ public class Sequence extends ASequence implements SequenceI
     {
       char[] oseq = seq.getSequence();
       initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
-              seq.getStart(),
-            seq.getEnd());
+              seq.getStart(), seq.getEnd());
     }
     description = seq.getDescription();
     if (seq != datasetSequence)
@@ -293,7 +296,6 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
-
   @Override
   public void setSequenceFeatures(SequenceFeature[] features)
   {
@@ -316,12 +318,11 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
-  public synchronized void addSequenceFeature(SequenceFeature sf)
+  public synchronized boolean addSequenceFeature(SequenceFeature sf)
   {
-    if (sequenceFeatures==null && datasetSequence != null)
+    if (sequenceFeatures == null && datasetSequence != null)
     {
-      datasetSequence.addSequenceFeature(sf);
-      return;
+      return datasetSequence.addSequenceFeature(sf);
     }
     if (sequenceFeatures == null)
     {
@@ -332,7 +333,7 @@ public class Sequence extends ASequence implements SequenceI
     {
       if (sequenceFeatures[i].equals(sf))
       {
-        return;
+        return false;
       }
     }
 
@@ -341,6 +342,9 @@ public class Sequence extends ASequence implements SequenceI
     temp[sequenceFeatures.length] = sf;
 
     sequenceFeatures = temp;
+
+    sequenceFeatureStore.add(sf);
+    return true;
   }
 
   @Override
@@ -348,12 +352,21 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (sequenceFeatures == null)
     {
-      if (datasetSequence!=null) {
-         datasetSequence.deleteFeature(sf);
+      if (datasetSequence != null)
+      {
+        datasetSequence.deleteFeature(sf);
       }
       return;
     }
 
+    /*
+     * new way
+     */
+    sequenceFeatureStore.delete(sf);
+
+    /*
+     * old way - to be removed
+     */
     int index = 0;
     for (index = 0; index < sequenceFeatures.length; index++)
     {
@@ -1094,7 +1107,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public SequenceI deriveSequence()
   {
-    Sequence seq=null;
+    Sequence seq = null;
     if (datasetSequence == null)
     {
       if (isValidDatasetSequence())
@@ -1108,7 +1121,7 @@ public class Sequence extends ASequence implements SequenceI
       else
       {
         // Create a new, valid dataset sequence
-       createDatasetSequence();
+        createDatasetSequence();
       }
     }
     return new Sequence(this);
@@ -1156,9 +1169,9 @@ public class Sequence extends ASequence implements SequenceI
       dsseq.setDescription(description);
       // move features and database references onto dataset sequence
       dsseq.sequenceFeatures = sequenceFeatures;
-      sequenceFeatures=null;
+      sequenceFeatures = null;
       dsseq.dbrefs = dbrefs;
-      dbrefs=null;
+      dbrefs = null;
       // TODO: search and replace any references to this sequence with
       // references to the dataset sequence in Mappings on dbref
       dsseq.pdbIds = pdbIds;
@@ -1416,15 +1429,14 @@ public class Sequence extends ASequence implements SequenceI
     return null;
   }
 
-
   @Override
   public List<DBRefEntry> getPrimaryDBRefs()
   {
-    if (datasetSequence!=null)
+    if (datasetSequence != null)
     {
       return datasetSequence.getPrimaryDBRefs();
     }
-    if (dbrefs==null || dbrefs.length==0)
+    if (dbrefs == null || dbrefs.length == 0)
     {
       return Collections.emptyList();
     }
@@ -1477,4 +1489,13 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
+  @Override
+  public List<SequenceFeature> findFeatures(String type, int from, int to)
+  {
+    if (datasetSequence != null)
+    {
+      return datasetSequence.findFeatures(type, from, to);
+    }
+    return sequenceFeatureStore.findFeatures(from, to, type);
+  }
 }